R/simpleheatmap.R

In protViz/quantable: Streamline Descriptive Analysis of Quantitative Data Matrices

#' heatmap2 facade
#' @export
#' @importFrom gplots heatmap.2
#' @param pln or dataframe with numerical values
#' @param distf distance function
#' @param hclustf clustering function
#' @param palette color palette
#' @param main title
#' @param labRow row labels
#' @param margins control margins of heatmap
#' @param scale c(row, column or none)
#' @param ... other parameters to heatmap.2
#' @examples
#' tmp = matrix(rep((1:100),times = 4) + rnorm(100*4,0,3),ncol=4)
#' mean = c(20,30,10,40)
#' sd = c(4,3,4,5)
#' tmp = sweep(tmp,2,sd,"*")
#' tmp = sweep(tmp,2,mean,"+")
#' par(mar=c(5,5,5,5))
#' simpleheatmap(tmp,ColSideColors=c("red","blue","pink","black"))
#' simpleheatmap(tmp)
simpleheatmap <- function(pln,
                          main="",
                          distf=dist,
                          hclustf=hclust,
                          labRow="",
                          palette=getBlueWhiteRed(),
                          margins=c(5,5),scale="none",...)
{
  heatmap.2(as.matrix(pln),
            trace="none",
            scale=scale,
            col=palette,
            labRow=labRow,
            cexRow=0.1 + 1/log10(dim(pln)[1]),
            cexCol=0.1 + 1/log10(dim(pln)[2]),
            distfun=distf,
            hclustfun=hclustf,
            margins=margins,
            main=main,
            ...=...)
  
}